Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate H281DRAFT_01451 H281DRAFT_01451 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__Burk376:H281DRAFT_01451 Length = 415 Score = 196 bits (499), Expect = 7e-55 Identities = 123/360 (34%), Positives = 182/360 (50%), Gaps = 20/360 (5%) Query: 4 LRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGT 63 +RN +G + I DL ++ G VLLGP+ GK++L+ +AGL T GSI G Sbjct: 50 VRNLTIRLGGNTVIENLDLDVQPGEFVVLLGPSGCGKSTLLHSIAGLIDVTDGSIEIAGE 109 Query: 64 DVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTP 123 D+T + R +A+V+Q + YP ++V N++ +RI+G A I R V +AAE+L+L P Sbjct: 110 DMTWADPKDRRIALVFQSYALYPTMSVERNLSFALRINGTPKAEIARRVARAAEMLQLGP 169 Query: 124 YLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGA 183 L R P LSGGQ+QR A+ RA+V+ A + L DEPL+NLD KLR ELR EL ++ + GA Sbjct: 170 LLKRKPAQLSGGQRQRVAIGRAIVREADVFLFDEPLSNLDAKLRTELRRELKQLHQRLGA 229 Query: 184 IFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLDVT 243 +Y T + EA++L A + G + QFG EVY RP NL A P +N ++ T Sbjct: 230 TMIYVTHDQVEAMMLATRMAVMRGGAIQQFGTPAEVYARPANLFVATFLGTPAMNLVNGT 289 Query: 244 ------------------KSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQ 285 S F SG + P + P P + + + P Sbjct: 290 LEQRDGALHFCTEQWRLDVSNYAFVDRSGESQPQSQPQS--PPRPCVLGVRAEDVRIGPT 347 Query: 286 TGDAARLQARTLVSEITGSESFVHLEYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAF 345 G+ A A+ + E G+ V L+Y GV+ + + P + LD+ H+ F Sbjct: 348 QGEGAGEHAKISLVEPMGNHRVVWLDYHGVQIASIDQSKTPVMPGDTLAFSLDSTHVSLF 407 Lambda K H 0.319 0.136 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 351 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 415 Length adjustment: 30 Effective length of query: 328 Effective length of database: 385 Effective search space: 126280 Effective search space used: 126280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory